Hello, I got a new Galaxy install using 17.01 latest. I wanted to get
the same tools as are in Galaxy main. I installed ephemeris with pip,
used get-tool-list to get a yml file with tools, and then shed-install
to my Galaxy server. After a few hours, 452 tools got successfully
installed, 0 skipped and 0 errored. However, when looking at Galaxy's
"manage installed tools", all of the tools that have dependencies are
in gray state - missing dependencies. (and error out if ran). If I
select a tool, and go to "repository actions", "manage tool
dependencies", I see that dependencies are marked as never installed.
If I select dependencies and click install, they install - really fast
(too fast?), and then that tool works fine... but I'm trying to
avoid manually telling each tool to install dependencies - there are a
lot of them :)
Any suggestions?